2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Moore J, Purcaro M, Pratt H, Epstein C, Shoresh N, Adrian J, Kawli T, Davis C, Dobin A, Kaul R, Halow J, Van Nostrand E, Freese P, Gorkin D, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams B, Mortazavi A, Keller C, Zhang X, Elhajjajy S, Huey J, Dickel D, Snetkova V, Wei X, Wang X, Rivera-Mulia J, Rozowsky J, Zhang J, Chhetri S, Zhang J, Victorsen A, White K, Visel A, Yeo G, Burge C, Lécuyer E, Gilbert D, Dekker J, Rinn J, Mendenhall E, Ecker J, Kellis M, Klein R, Noble W, Kundaje A, Guigó R, Farnham P, Cherry J, Myers R, Ren B, Graveley B, Gerstein M, Pennacchio L, Snyder M, Bernstein B, Wold B, Hardison R, Gingeras T, Stamatoyannopoulos J, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020, 583: 699-710. PMID: 32728249, PMCID: PMC7410828, DOI: 10.1038/s41586-020-2493-4.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinDatabases, GeneticDeoxyribonuclease IDNADNA FootprintingDNA MethylationDNA Replication TimingGenomeGenome, HumanGenomicsHistonesHumansMiceMice, TransgenicMolecular Sequence AnnotationRegistriesRegulatory Sequences, Nucleic AcidRNA-Binding ProteinsTranscription, GeneticTransposasesConceptsMouse genomeCandidate cis-regulatory elementsCis-regulatory elementsDNA Elements (ENCODE) projectMouse fetal developmentChromatin structureGene regulationRespective genomesCellular contextDNA elementsDNA methylationENCODE dataTranscription factorsRNA transcriptionWeb-based serverGenomeExpansive resourceRNAEncyclopediaProteinFetal developmentChromatinTranscriptionHumansMethylation
2016
Fine‐scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer
Shi J, Zhang Y, Zheng W, Michailidou K, Ghoussaini M, Bolla M, Wang Q, Dennis J, Lush M, Milne R, Shu X, Beesley J, Kar S, Andrulis I, Anton‐Culver H, Arndt V, Beckmann M, Zhao Z, Guo X, Benitez J, Beeghly‐Fadiel A, Blot W, Bogdanova N, Bojesen S, Brauch H, Brenner H, Brinton L, Broeks A, Brüning T, Burwinkel B, Cai H, Canisius S, Chang‐Claude J, Choi J, Couch F, Cox A, Cross S, Czene K, Darabi H, Devilee P, Droit A, Dork T, Fasching P, Fletcher O, Flyger H, Fostira F, Gaborieau V, García‐Closas M, Giles G, Grip M, Guenel P, Haiman C, Hamann U, Hartman M, Miao H, Hollestelle A, Hopper J, Hsiung C, Investigators K, Ito H, Jakubowska A, Johnson N, Torres D, Kabisch M, Kang D, Khan S, Knight J, Kosma V, Lambrechts D, Li J, Lindblom A, Lophatananon A, Lubinski J, Mannermaa A, Manoukian S, Le Marchand L, Margolin S, Marme F, Matsuo K, McLean C, Meindl A, Muir K, Neuhausen S, Nevanlinna H, Nord S, Børresen‐Dale A, Olson J, Orr N, van den Ouweland A, Peterlongo P, Putti T, Rudolph A, Sangrajrang S, Sawyer E, Schmidt M, Schmutzler R, Shen C, Hou M, Shrubsole M, Southey M, Swerdlow A, Teo S, Thienpont B, Toland A, Tollenaar R, Tomlinson I, Truong T, Tseng C, Wen W, Winqvist R, Wu A, Yip C, Zamora P, Zheng Y, Floris G, Cheng C, Hooning M, Martens J, Seynaeve C, Kristensen V, Hall P, Pharoah P, Simard J, Chenevix‐Trench G, Dunning A, Antoniou A, Easton D, Cai Q, Long J. Fine‐scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer. International Journal Of Cancer 2016, 139: 1303-1317. PMID: 27087578, PMCID: PMC5110427, DOI: 10.1002/ijc.30150.Peer-Reviewed Original ResearchConceptsIndependent association signalsAssociation signalsGenome-wide association studiesFunctional genomics dataPrevious genome-wide association studyEuropean ancestryDNA Elements (ENCODE) projectBreast cancer susceptibility lociFine-mapping studiesCancer susceptibility lociFine-scale mappingIndependent risk variantsRoadmap EpigenomicsCancer Genome AtlasGenomic dataIntegrative analysisAssociation studiesSusceptibility lociFunctional variantsBreast cancer susceptibilityRisk variantsGenome AtlasCancer susceptibilityBreast Cancer Association ConsortiumAncestry
2012
An integrated encyclopedia of DNA elements in the human genome
Dunham I, Kundaje A, Aldred S, Collins P, Davis C, Doyle F, Epstein C, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie B, Landt S, Lee B, Pauli F, Rosenbloom K, Sabo P, Safi A, Sanyal A, Shoresh N, Simon J, Song L, Trinklein N, Altshuler R, Birney E, Brown J, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey T, Gerstein M, Giardine B, Greven M, Hardison R, Harris R, Herrero J, Hoffman M, Iyer S, Kellis M, Khatun J, Kheradpour P, Kundaje A, Lassmann T, Li Q, Lin X, Marinov G, Merkel A, Mortazavi A, Parker S, Reddy T, Rozowsky J, Schlesinger F, Thurman R, Wang J, Ward L, Whitfield T, Wilder S, Wu W, Xi H, Yip K, Zhuang J, Bernstein B, Birney E, Dunham I, Green E, Gunter C, Snyder M, Pazin M, Lowdon R, Dillon L, Adams L, Kelly C, Zhang J, Wexler J, Green E, Good P, Feingold E, Bernstein B, Birney E, Crawford G, Dekker J, Elnitski L, Farnham P, Gerstein M, Giddings M, Gingeras T, Green E, Guigó R, Hardison R, Hubbard T, Kellis M, Kent W, Lieb J, Margulies E, Myers R, Snyder M, Stamatoyannopoulos J, Tenenbaum S, Weng Z, White K, Wold B, Khatun J, Yu Y, Wrobel J, Risk B, Gunawardena H, Kuiper H, Maier C, Xie L, Chen X, Giddings M, Bernstein B, Epstein C, Shoresh N, Ernst J, Kheradpour P, Mikkelsen T, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne M, Durham T, Ku M, Truong T, Ward L, Altshuler R, Eaton M, Kellis M, Djebali S, Davis C, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov G, Khatun J, Williams B, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid R, Alioto T, Antoshechkin I, Baer M, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood M, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo O, Park E, Preall J, Presaud K, Ribeca P, Risk B, Robyr D, Ruan X, Sammeth M, Sandhu K, Schaeffer L, See L, Shahab A, Skancke J, Suzuki A, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis S, Hannon G, Giddings M, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras T, Rosenbloom K, Sloan C, Learned K, Malladi V, Wong M, Barber G, Cline M, Dreszer T, Heitner S, Karolchik D, Kent W, Kirkup V, Meyer L, Long J, Maddren M, Raney B, Furey T, Song L, Grasfeder L, Giresi P, Lee B, Battenhouse A, Sheffield N, Simon J, Showers K, Safi A, London D, Bhinge A, Shestak C, Schaner M, Ki Kim S, Zhang Z, Mieczkowski P, Mieczkowska J, Liu Z, McDaniell R, Ni Y, Rashid N, Kim M, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer V, Lieb J, Crawford G, Li G, Sandhu K, Zheng M, Wang P, Luo O, Shahab A, Fullwood M, Ruan X, Ruan Y, Myers R, Pauli F, Williams B, Gertz J, Marinov G, Reddy T, Vielmetter J, Partridge E, Trout D, Varley K, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling K, Anaya M, Cross M, King B, Muratet M, Antoshechkin I, Newberry K, McCue K, Nesmith A, Fisher-Aylor K, Pusey B, DeSalvo G, Parker S, Balasubramanian S, Davis N, Meadows S, Eggleston T, Gunter C, Newberry J, Levy S, Absher D, Mortazavi A, Wong W, Wold B, Blow M, Visel A, Pennachio L, Elnitski L, Margulies E, Parker S, Petrykowska H, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez J, Griffiths E, Harte R, Hendrix D, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin M, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez J, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanari E, Tress M, van Baren M, Walters N, Washietl S, Wilming L, Zadissa A, Zhang Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Reymond A, Guigó R, Harrow J, Hubbard T, Landt S, Frietze S, Abyzov A, Addleman N, Alexander R, Auerbach R, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle A, Cao A, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming J, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyengar S, Jin V, Karczewski K, Kasowski M, Lacroute P, Lam H, Lamarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu X, O’Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan K, Yang X, Yip K, Zhang Z, Struhl K, Weissman S, Gerstein M, Farnham P, Snyder M, Tenenbaum S, Penalva L, Doyle F, Karmakar S, Landt S, Bhanvadia R, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, White K, Auer T, Centanin L, Eichenlaub M, Gruhl F, Heermann S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield T, Wang J, Collins P, Aldred S, Trinklein N, Partridge E, Myers R, Dekker J, Jain G, Lajoie B, Sanyal A, Balasundaram G, Bates D, Byron R, Canfield T, Diegel M, Dunn D, Ebersol A, Frum T, Garg K, Gist E, Hansen R, Boatman L, Haugen E, Humbert R, Jain G, Johnson A, Johnson E, Kutyavin T, Lajoie B, Lee K, Lotakis D, Maurano M, Neph S, Neri F, Nguyen E, Qu H, Reynolds A, Roach V, Rynes E, Sabo P, Sanchez M, Sandstrom R, Sanyal A, Shafer A, Stergachis A, Thomas S, Thurman R, Vernot B, Vierstra J, Vong S, Wang H, Weaver M, Yan Y, Zhang M, Akey J, Bender M, Dorschner M, Groudine M, MacCoss M, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos J, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe N, Sobral D, Vaquerizas J, Wilder S, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Schaub M, Kundaje A, Hardison R, Miller W, Giardine B, Harris R, Wu W, Bickel P, Banfai B, Boley N, Brown J, Huang H, Li Q, Li J, Noble W, Bilmes J, Buske O, Hoffman M, Sahu A, Kharchenko P, Park P, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi H, Zhuang J, Gerstein M, Alexander R, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu X, Rozowsky J, Yan K, Yip K, Birney E. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489: 57-74. PMID: 22955616, PMCID: PMC3439153, DOI: 10.1038/nature11247.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAnimalsBinding SitesChromatinChromatin ImmunoprecipitationChromosomes, HumanDeoxyribonuclease IDNADNA FootprintingDNA MethylationDNA-Binding ProteinsEncyclopedias as TopicExonsGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyGenome, HumanGenomicsHistonesHumansMammalsMolecular Sequence AnnotationNeoplasmsPolymorphism, Single NucleotidePromoter Regions, GeneticProteinsRegulatory Sequences, Nucleic AcidSequence Analysis, RNATranscription FactorsTranscription, GeneticConceptsHuman genomeRegions of transcriptionTranscription factor associationDNA Elements (ENCODE) projectProtein-coding regionsBlueprint of lifeCandidate regulatory elementsChromatin structureHistone modificationsGene regulationFunctional annotationDNA elementsBiochemical functionsNew insightsRegulatory elementsGenomeHuman diseasesExpansive resourceGenesEncyclopediaRegulationBiomedical researchTranscriptionAnnotationInsights
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